Why is render stacking less efficient (noisier) than rendering normally?
Cycles uses Quasi Monte Carlo sampling:

http://en.wikipedia.org/wiki/Quasi-Monte_Carlo_method

That means it will try to evenly distribute samples so rendering converges faster. If you render multiple times with different seeds however then this even distribution is lost because it mixes different distributions without ensuring that the combined result is even too.

Since Blender 2.78 there is a sample offset command line option to avoid that problem, where you can set it so that each render uses a subset of samples from the same distribution.